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Mehra P, Kumar A. Emerging importance of stool preservation methods in OMICS studies with special focus on cancer biology. Cell Biochem Funct 2024; 42:e4063. [PMID: 38961596 DOI: 10.1002/cbf.4063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/12/2024] [Accepted: 05/18/2024] [Indexed: 07/05/2024]
Abstract
The intricate consortium of microorganisms in the human gut plays a crucial role in different physiological functions. The complex known-unknown elements of the gut microbiome are perplexing and the absence of standardized procedures for collecting and preserving samples has hindered continuous research in comprehending it. The technological bias produced because of lack of standard protocols has affected the reproducibility of results. The complex nature of diseases like colorectal cancer, gastric cancer, hepatocellular carcinoma and breast cancer require a thorough understanding of its etiology for an efficient and timely diagnosis. The designated protocols for collection and preservation of stool specimens have great variance, hence generate inconsistencies in OMICS studies. Due to the complications associated to the nature of sample, it is important to preserve the sample to be studied later in a laboratory or to be used in the future research purpose. Stool preservation is gaining importance due to the increased use of treatment options like fecal microbiota transplantation to cure conditions like recurrent Clostridium difficile infections and for OMICS studies including metagenomics, metabolomics and culturomics. This review provides an insight into the importance of omics studies for the identification and development of novel biomarkers for quick and noninvasive diagnosis of various diseases.
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Affiliation(s)
- Parul Mehra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
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Jørgensen AB, Jonsson I, Friis-Hansen L, Brandstrup B. Collagenase-producing bacteria are common in anastomotic leakage after colorectal surgery: a systematic review. Int J Colorectal Dis 2023; 38:275. [PMID: 38038731 PMCID: PMC10692267 DOI: 10.1007/s00384-023-04562-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2023] [Indexed: 12/02/2023]
Abstract
PURPOSE Some gut bacteria can produce enzymes (collagenases) that can break down collagen in the intestinal wall. This could be a part of the pathophysiology of anastomotic leakage (AL). This systematic review aimed to investigate if such bacteria were present more frequently in AL patients versus non-AL patients following colorectal surgery. METHODS This systematic review was reported according to the PRISMA and AMSTAR guidelines. Before the literature search, a study protocol was registered at PROSPERO (CRD42022363454). We searched PubMed, EMBASE, Google Scholar, and Cochrane CENTRAL on April 9th, 2023, for randomized and observational human studies of AL following colorectal surgery with information on gastrointestinal bacteria. The primary outcome was bacteria with the potential to produce collagenase. The risk of bias was assessed with the Newcastle-Ottawa Scale, as all studies were observational. RESULTS We included 15 studies, with a total of 52,945 patients, of which 1,747 had AL, and bacteriological information from feces, mucosa, the resected specimen, or drain fluid was presented. In 10 of the 15 studies, one or more collagenase-producing bacteria were identified in the patients with AL. Neither the bacteria nor the collagenase production were quantified in any of the studies. The studies varied greatly in terms of sample material, analytical method, and time of collection. Studies using DNA sequencing methods did not report findings of collagenase-producing bacteria. CONCLUSION Collagenase-producing bacteria are more common in patients with AL following colorectal surgery than in patients without AL, but the significance is unclear. From the current studies, it is not possible to determine the pathogenicity of the individual gut bacteria.
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Affiliation(s)
- Anders Bech Jørgensen
- Department of Surgery, Holbæk Hospital, Part of Copenhagen University Hospitals, Region Zealand, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Isabella Jonsson
- Department of Surgery, Holbæk Hospital, Part of Copenhagen University Hospitals, Region Zealand, Denmark
| | - Lennart Friis-Hansen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Bispebjerg and Frederiksberg University Hospital, Capital Region, Frederiksberg, Denmark
- Department of Microbiology, Rigshospitalet, Capital Region, Denmark
| | - Birgitte Brandstrup
- Department of Surgery, Holbæk Hospital, Part of Copenhagen University Hospitals, Region Zealand, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Labossiere A, Ramsey M, Merritt J, Kreth J. Molecular commensalism-how to investigate underappreciated health-associated polymicrobial communities. mBio 2023; 14:e0134223. [PMID: 37754569 PMCID: PMC10653818 DOI: 10.1128/mbio.01342-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
The study of human commensal bacteria began with the first observation of prokaryotes >340 years ago. Since then, the study of human-associated microbes has been justifiably biased toward the study of infectious pathogens. However, the role of commensal microbes has in recent years begun to be understood with some appreciation of them as potential protectors of host health rather than bystanders. As our understanding of these valuable microbes grows, it highlights how much more remains to be learned about them and their roles in maintaining health. We note here that a thorough framework for the study of commensals, both in vivo and in vitro is overall lacking compared to well-developed methodologies for pathogens. The modification and application of methods for the study of pathogens can work well for the study of commensals but is not alone sufficient to properly characterize their relationships. This is because commensals live in homeostasis with the host and within complex communities. One difficulty is determining which commensals have a quantifiable impact on community structure and stability as well as host health, vs benign microbes that may indeed serve only as bystanders. Human microbiomes are composed of bacteria, archaea, fungi, and viruses. This review focuses particularly on oral bacteria, yet many of the principles of commensal impacts on host health observed in the mouth can translate well to other host sites. Here, we discuss the value of commensals, the shortcomings involved in model systems for their study, and some of the more notable impacts they have upon not only each other but host health.
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Affiliation(s)
- Alex Labossiere
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Matthew Ramsey
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Justin Merritt
- Biomaterial and Biomedical Sciences, Oregon Health and Science University, School of Dentistry, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health and Science University, Portland, Oregon, USA
| | - Jens Kreth
- Biomaterial and Biomedical Sciences, Oregon Health and Science University, School of Dentistry, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health and Science University, Portland, Oregon, USA
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Huang Z, Chang Y, Hao K, Tan Y, Ding L, Wang L, Wang Z, Pan Z, Gao H, Wu J, Zhu Y, Gao Q, Bi Y, Yang R. Immunomagnetic-bead enriched culturomics (IMBEC) for isolating pathobionts from feces of colorectal cancer patients. IMETA 2023; 2:e100. [PMID: 38868439 PMCID: PMC10989793 DOI: 10.1002/imt2.100] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 06/14/2024]
Abstract
Culturomics employs various cultivating conditions to obtain different types of bacteria and new species. However, current culturomics lacks a highly efficient method for isolating specific pathobionts. Immunomagnetic bead technology, which uses magnetic beads conjugated with antibodies for capturing the antigen to realize enrichment of the targets, has been employed as an alternative method. In this study, we developed a novel method, immunomagnetic bead-enriched culturomics (IMBEC), in which magnetic bead-conjugated antibodies purified from the fecal samples of patients with colorectal cancer (CRC) were used to enrich and isolate potential pathobionts. A protocol for enriching potential pathobionts via immunomagnetic capture was developed by optimizing the concentrations of coupling reagents, NaCl, and detergent. The efficacy of pathobiont enrichment was compared between antibody-coated magnetic beads (antibody group) and nonconjugated blank magnetic beads (blank group). To determine the proinflammatory potential of isolates from both groups, we investigated their ability to induce cytokine production in THP-1 macrophages. This protocol was employed for isolating bacteria from 10 fecal samples of patients with CRC, which were simultaneously compared with those isolated from the blank group. A total of 209 bacterial species were isolated from both groups, including 173 from the antibody group, 160 from the blank group, and 124 from both groups. Bacteria isolated from the antibody group produced more proinflammatory cytokines than those isolated from the blank group. IMBEC is a promising method for relatively specific isolation of potential pathobionts for a particular disease of interest.
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Affiliation(s)
- Ziran Huang
- The Key and Characteristic Laboratory of Modern Pathogen Biology, School of Basic Medical SciencesGuizhou Medical UniversityGuiyangChina
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Yuxiao Chang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Kun Hao
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (BZ0329)BeijingChina
| | - Yafang Tan
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (BZ0329)BeijingChina
| | - Lei Ding
- Beijing Shijitan HospitalCapital Medical UniversityBeijingChina
| | - Likun Wang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Zhen Wang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Zhiyuan Pan
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Hong Gao
- Beijing Shijitan HospitalCapital Medical UniversityBeijingChina
| | - Jiahong Wu
- The Key and Characteristic Laboratory of Modern Pathogen Biology, School of Basic Medical SciencesGuizhou Medical UniversityGuiyangChina
| | - Yubing Zhu
- Beijing Shijitan HospitalCapital Medical UniversityBeijingChina
| | - Qi Gao
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (BZ0329)BeijingChina
| | - Yujing Bi
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (BZ0329)BeijingChina
| | - Ruifu Yang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (BZ0329)BeijingChina
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Wan X, Yang Q, Wang X, Bai Y, Liu Z. Isolation and Cultivation of Human Gut Microorganisms: A Review. Microorganisms 2023; 11:microorganisms11041080. [PMID: 37110502 PMCID: PMC10141110 DOI: 10.3390/microorganisms11041080] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/12/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Microbial resources from the human gut may find use in various applications, such as empirical research on the microbiome, the development of probiotic products, and bacteriotherapy. Due to the development of "culturomics", the number of pure bacterial cultures obtained from the human gut has significantly increased since 2012. However, there is still a considerable number of human gut microbes to be isolated and cultured. Thus, to improve the efficiency of obtaining microbial resources from the human gut, some constraints of the current methods, such as labor burden, culture condition, and microbial targetability, still need to be optimized. Here, we overview the general knowledge and recent development of culturomics for human gut microorganisms. Furthermore, we discuss the optimization of several parts of culturomics including sample collection, sample processing, isolation, and cultivation, which may improve the current strategies.
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Affiliation(s)
- Xuchun Wan
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qianqian Yang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiangfeng Wang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yun Bai
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhi Liu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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A new method for screening and culture of Clostridium from pit mud under non-anaerobic conditions. J Microbiol Methods 2022; 200:106559. [PMID: 36007702 DOI: 10.1016/j.mimet.2022.106559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/19/2022] [Accepted: 08/19/2022] [Indexed: 12/27/2022]
Abstract
Strong-flavor Baijiu (SFB) is produced in complex fermentation in pits under ground. Clostridium producing hexanoic acid plays a key role in the flavor formation of SFB. The screening and culture for Clostridium are very difficult because of its strict anaerobic characteristics. In this study, electric field assisted screening (EFAS) was used to screen Clostridium from pit mud, and electric culture (EC) was used to cultivate Clostridium under non-anaerobic conditions. A strain with a high yield of hexanoic acid was screened and named as Clostridium sp. EFAS6. Under non-anaerobic conditions, it grew rapidly only near the cathode end in the EFAS device because of the low oxidation-reduction potential of that electrode. In the experiment of high-density culture in the EC device, the cell concentration reached 106-107. After energy consumption was calculated, the optimal loading voltage was found to be 10 V. In the application, the broth of Clostridium sp. EFAS6 increased the content of ethyl hexanoic in SFB. Under non-anaerobic conditions, the anaerobe was screened by EFAS and cultivated in high density by EC. The EFAS and EC could also be used for the screening and culture of other anaerobes under non-anaerobic conditions.
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Sancak B, Cenk Mirza H, Altun B, Tunçkanat F. Identification and distribution of anaerobic bacteria isolated from clinical specimens in a University Hospital: 4 years’ experience. MICROBIOLOGY INDEPENDENT RESEARCH JOURNAL 2022. [DOI: 10.18527/2500-2236-2022-9-1-75-81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Anaerobes, which are components of microbiota, can cause life-threatening infections. Because of their fastidious nature, they are difficult to isolate and are often overlooked. The goal of this study was to identify the anaerobic bacteria isolated from clinical specimens at the Central Laboratory of Hacettepe University Hospital in 2015-2018 and to evaluate the distribution of the isolated bacterial species among the different specimen types. The anaerobic bacteria isolated from the specimens were identified by the conventional methods and MALDI-TOF MS.Overall, 15,300 anaerobic cultures were studied. Of these, 14,434 (94.3%) were blood samples and 866 (5.7%) were other clinical specimens. A total of 138 anaerobic bacteria were isolated: 62 (44.9%) were isolated from blood samples and 76 (55.1%) from other specimens. The most isolated anaerobes from blood cultures were Bacteroides spp. (41.9%), followed by Cutibacterium acnes (25.8%) and Clostridium spp. (9.7%). The most isolated anaerobes from the other specimens were Gram-negative bacilli, including Bacteroides spp. (15.8%), Fusobacterium spp. (14.5%), Prevotella spp. (14.5%), and Porphyromonas spp. (2.6%). Anaerobic Finegoldia magna represented the major species among the isolated Gram-positive bacteria (10.5%). Anaerobic growth was observed in 0.4% of all the blood cultures and in 5.8% of the positive blood cultures. The results of our study showed that the incidence of anaerobic bacteremia was stable during the 2015-2018 period.
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Hernalsteens S, Huang S, Cong HH, Chen XD. The final fate of food: On the establishment of in vitro colon models. Food Res Int 2021; 150:110743. [PMID: 34865762 DOI: 10.1016/j.foodres.2021.110743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/24/2021] [Accepted: 10/06/2021] [Indexed: 02/07/2023]
Abstract
The search for life/health quality has driven the search for a better understanding of food components on the overall individual health, which turns to be intrinsically related to the digestive system. In vitro digestion models are considered an alternative for the in vivo studies for a variety of practical reasons, but further research is still needed concerning the colon model establishment. An effective in vitro colon model should consider all unit operations and transport phenomena, together with chemical and biochemical reactions, material handling and reactor design. Due to the different techniques and dependence on the donor microbiota, it is difficult to obtain a standard protocol with results reproductible in time and space. Furthermore, the colon model should be fed with a representative substrate, thus what happens in upper digestion tract and absorption prior to colon is also of crucial importance. Essentially, there are two ways to think about how to achieve a good and useful in vitro colon model: a complex biomimetic system that provides results comparable with the in vivo studies or a simple system, that despite the fact it could not give physiologically relevant data, it is sufficient to understand the fate of some specific components.
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Affiliation(s)
- Saartje Hernalsteens
- College of Chemistry, Chemical Engineering and Materials Science - Soochow University, China.
| | | | - Hai Hua Cong
- College of Food Science and Engineering - Dalian Ocean University, China
| | - Xiao Dong Chen
- College of Chemistry, Chemical Engineering and Materials Science - Soochow University, China.
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9
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Updating the repertoire of cultured bacteria from the human being. Microb Pathog 2020; 150:104698. [PMID: 33347961 DOI: 10.1016/j.micpath.2020.104698] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 12/19/2022]
Abstract
The recent renewal of cultural approach has substantially enriched knowledge of the human microbiota, notably through the discovery of new taxa from various anatomical sites. As an increasing number of these recent species are currently considered beneficial or harmful for human health, a constant updating of the repertoire of bacteria and archaea isolated from humans by culture is essential. Herein, we show that the number of cultured bacterial species associated with human beings increased, from 2776 in 2018, to 3253 in 2020, representing a 17% increase in 2 years by adding 477 species, of which 64% are new species (N = 307). A wide majority of the species added (i.e., 63%) were isolated using the culturomics approach, while 16% were cultured as part of clinical microbiology laboratories. Human microbiota studies would benefit from the completeness of the repertoire of bacteria associated with human beings, which would require continued efforts to culture microbes from human specimens.
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Characterization of medical relevant anaerobic microorganisms by isothermal microcalorimetry. Anaerobe 2020; 66:102282. [PMID: 33017653 DOI: 10.1016/j.anaerobe.2020.102282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/27/2020] [Accepted: 10/01/2020] [Indexed: 12/20/2022]
Abstract
Detection of anaerobe bacteria by culture methods requires appropriate media, special growth conditions, additional detection techniques and it typically takes several days. Therefore, anaerobes are often missed in patient specimens under routine culture conditions. Microcalorimetry may provide a simple and accurate real-time method for faster and better detection of anaerobes. An isothermal calorimeter which detect minimal changes of temperature over time was used for the calorimetric experiments. In order to find optimal growth conditions, seven reference or clinical strains of medical relevant anaerobe bacteria were tested under different circumstances. First, the strains were tested with different growth media. After determining the optimal medium for each strain, the gas phase was modified by adding 3 mL or 4 mL medium, to evaluate growth under conditions with less oxygen. Cooked Meat Medium was best supporting growth of the tested strains, including Cutibacterium acnes, Fusobacterium nucleatum, Finegoldia magna, Parvimonas micra, Bacteroides fragilis and Actinomyces odontolyticus, followed by thioglycolate. The best medium to detect Clostridioides difficile was H-Medium. All tested strains showed better growth in 4 mL medium than in 3 mL. The detection time ranged between 10 and 72 h. Our results demonstrated that the sensitivity and the detection time of anaerobe bacteria can be improved by isothermal calorimetry with optimization of growth conditions. Therefore, calorimetric detection, a practical, quick and easy-to-do method, has the potential to replace current microbiological methods.
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Optimization and standardization of the culturomics technique for human microbiome exploration. Sci Rep 2020; 10:9674. [PMID: 32541790 PMCID: PMC7295790 DOI: 10.1038/s41598-020-66738-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/26/2020] [Indexed: 12/16/2022] Open
Abstract
Culturomics is a high-throughput culture approach that has dramatically contributed to the recent renewal of culture. While metagenomics enabled substantial advances in exploring the microbiota, culturomics significantly expanded our knowledge regarding the bacterial gut repertoire through the discovery and the description of hundreds of new taxa. While this approach relies on the variation of culture conditions and media, we have tested so far more than 300 conditions since the beginning of culturomics studies. In this context, we aimed herein to identify the most profitable conditions for optimizing culturomics approach. For this purpose, we have analysed a set of 58 culturomics conditions that were previously applied to 8 faecal specimens, enabling the isolation of 497 bacterial species. As a result, we were able to reduce the number of conditions used to isolate these 497 of more than a half (i.e. to 25 culture conditions). We have also established a list of the 16 conditions that allowed to capture 98% of the total number of species previously isolated. These data constitute a methodological starting point for culture-based microbiota studies by improving the culturomics workflow without any loss of captured bacterial diversity.
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Khattab RA, Ahmed NA, Ragab YM, Rasmy SA. Bacteria producing antimicrobials against Clostridium difficile isolated from human stool. Anaerobe 2020; 63:102206. [PMID: 32339663 DOI: 10.1016/j.anaerobe.2020.102206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 11/30/2022]
Abstract
Clostridium difficile infection (CDI) is a common cause of morbidity and mortality in hospitalized patients worldwide. The major problem facing current treatment is multiple recurrences, prompting the need for alternative therapies. In this study we isolated bacterial species, from Egyptian individuals' stool, with antimicrobial activity against clinical isolates of C. difficile and tried to examine the nature of the produced antimicrobials. In vitro antibacterial activity against C. difficile was initially screened in 123 fecal samples cultures using an agar overlay method. The isolates with antimicrobial activity against C. difficile in addition to Clostridium isolates were identified using partial 16S rDNA gene sequencing analysis. The isolates acting against C. difficile belonged to Lactobacillus, Enterococcus and Clostridium genera. The concentrated cell-free supernatants (CFSs) from these bacterial isolates were examined for antimicrobial activity against C. difficile growth by broth dilution method. 10 x concentrated CFSs of five isolates showed inhibition for C. difficile growth which was significantly different (p < 0.001) from control. Lactobacillus agilis T99A and Clostridium butyricum T58A isolates were selected for further evaluation of the produced antimicrobials. The antimicrobial activity of 10x CFSs of the two isolates was stable after enzymatic treatment with proteinase K or heating treatments up to 90 °C or neutralizing pH. The spectrum of activity of the two isolates was evaluated using different gram-positive and gram-negative bacterial species and did not show antimicrobial activity against these species. Our results showed two unconventional bacterial isolates: L. agilis T99A and C. butyricum T58A producing extracellular thermo stable antimicrobial agents against C. difficile clinical isolates.
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Affiliation(s)
- Rania Abdelmonem Khattab
- Microbiology and Immunology Department, Faculty of Pharmacy, Cairo University, Kasr Al-Aini, 11562, Cairo, Egypt.
| | - Noha A Ahmed
- Microbiology and Immunology Department, Faculty of Pharmacy, Cairo University, Kasr Al-Aini, 11562, Cairo, Egypt
| | - Yasser M Ragab
- Microbiology and Immunology Department, Faculty of Pharmacy, Cairo University, Kasr Al-Aini, 11562, Cairo, Egypt
| | - Salwa A Rasmy
- Microbiology and Immunology Department, Faculty of Pharmacy, Cairo University, Kasr Al-Aini, 11562, Cairo, Egypt
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Abstract
The microbiome has received increasing attention over the last 15 years. Although gut microbes have been explored for several decades, investigations of the role of microorganisms that reside in the human gut has attracted much attention beyond classical infectious diseases. For example, numerous studies have reported changes in the gut microbiota during not only obesity, diabetes, and liver diseases but also cancer and even neurodegenerative diseases. The human gut microbiota is viewed as a potential source of novel therapeutics. Between 2013 and 2017, the number of publications focusing on the gut microbiota was, remarkably, 12 900, which represents four-fifths of the total number of publications over the last 40 years that investigated this topic. This review discusses recent evidence of the impact of the gut microbiota on metabolic disorders and focus on selected key mechanisms. This review also aims to provide a critical analysis of the current knowledge in this field, identify putative key issues or problems and discuss misinterpretations. The abundance of metagenomic data generated on comparing diseased and healthy subjects can lead to the erroneous claim that a bacterium is causally linked with the protection or the onset of a disease. In fact, environmental factors such as dietary habits, drug treatments, intestinal motility and stool frequency and consistency are all factors that influence the composition of the microbiota and should be considered. The cases of the bacteria Prevotella copri and Akkermansia muciniphila will be discussed as key examples.
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Affiliation(s)
- Patrice D Cani
- Metabolism and Nutrition Research Group, Université catholique de Louvain, WELBIO-Walloon Excellence in Life Sciences and BIOtechnology, Louvain Drug Research Institute, Brussels, Belgium
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